Variant report

Variant	rs10513561
Chromosome Location	chr3:160711091-160711092
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 61 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:59)

rs_ID	r²[population]
rs10513557	1.00[CHD][hapmap]
rs10513562	0.90[JPT][hapmap]
rs12374096	1.00[CEU][hapmap];0.80[EUR][1000 genomes]
rs12374192	1.00[CEU][hapmap];0.80[EUR][1000 genomes]
rs12486103	1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs12487156	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];0.83[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12488403	1.00[CHD][hapmap];1.00[JPT][hapmap]
rs12488621	0.87[LWK][hapmap]
rs12493266	0.92[AFR][1000 genomes];0.89[AMR][1000 genomes]
rs12496235	0.90[JPT][hapmap]
rs1345155	1.00[CEU][hapmap];0.88[EUR][1000 genomes]
rs1447612	1.00[CHD][hapmap]
rs16831552	1.00[CHD][hapmap]
rs16831555	0.87[CHD][hapmap]
rs16831581	1.00[JPT][hapmap]
rs16831611	1.00[CHD][hapmap];1.00[JPT][hapmap]
rs16831645	0.87[LWK][hapmap];0.81[MKK][hapmap];0.88[YRI][hapmap]
rs16831799	1.00[JPT][hapmap];0.81[YRI][hapmap];0.89[AFR][1000 genomes];0.84[AMR][1000 genomes]
rs16831850	0.90[JPT][hapmap];0.81[AMR][1000 genomes]
rs16831864	0.90[JPT][hapmap];0.81[AMR][1000 genomes]
rs17236697	0.80[EUR][1000 genomes]
rs17236711	0.81[EUR][1000 genomes]
rs17392097	1.00[CEU][hapmap];0.96[EUR][1000 genomes]
rs17826388	1.00[CEU][hapmap];0.80[EUR][1000 genomes]
rs17826412	0.80[EUR][1000 genomes]
rs17826418	1.00[CEU][hapmap];0.88[EUR][1000 genomes]
rs17826424	0.88[EUR][1000 genomes]
rs3925722	0.90[JPT][hapmap];0.84[AMR][1000 genomes]
rs56741972	0.80[EUR][1000 genomes]
rs56807417	0.97[AFR][1000 genomes];0.89[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs57655051	0.96[EUR][1000 genomes]
rs58739937	0.82[EUR][1000 genomes]
rs59593286	0.81[AMR][1000 genomes]
rs60811584	0.80[EUR][1000 genomes]
rs62282277	0.84[EUR][1000 genomes]
rs6441350	0.90[JPT][hapmap];0.81[AMR][1000 genomes]
rs6441363	1.00[CEU][hapmap];0.89[CHB][hapmap]
rs6771581	0.84[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs6773813	0.88[AFR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6787599	1.00[JPT][hapmap]
rs6790705	1.00[JPT][hapmap];0.94[YRI][hapmap];0.97[AFR][1000 genomes];0.89[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs6796168	0.81[ASW][hapmap];0.90[JPT][hapmap];0.87[LWK][hapmap]
rs6806054	0.90[JPT][hapmap]
rs6806729	0.92[ASW][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];0.95[MKK][hapmap];0.81[YRI][hapmap]
rs6807796	1.00[JPT][hapmap]
rs73019384	0.97[AFR][1000 genomes];0.89[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs7627500	0.92[ASW][hapmap];0.85[CHD][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];0.95[MKK][hapmap];0.94[YRI][hapmap];0.95[AFR][1000 genomes];0.89[AMR][1000 genomes]
rs7632423	0.90[JPT][hapmap]
rs7639529	0.88[AFR][1000 genomes];0.89[AMR][1000 genomes]
rs778653	0.90[JPT][hapmap]
rs778657	0.90[JPT][hapmap]
rs935499	1.00[JPT][hapmap]
rs9682249	0.84[AMR][1000 genomes]
rs9682995	0.85[AFR][1000 genomes];0.89[AMR][1000 genomes]
rs9811594	0.90[JPT][hapmap]
rs9818992	0.90[JPT][hapmap]
rs9826857	0.90[JPT][hapmap]
rs9830183	0.89[JPT][hapmap]
rs9875200	0.90[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv931072	chr3:160669567-161159779	Enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	98 gene(s)	inside rSNPs	diseases
2	nsv1007004	chr3:160695108-160718154	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10513561	HPS3	trans	brain	seeQTL

Chromatin state (count:7 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:160705000-160720000	Weak transcription	Gastric	stomach
2	chr3:160706000-160711200	Weak transcription	Right Atrium	heart
3	chr3:160706400-160716000	Weak transcription	Primary T cells from cord blood	blood
4	chr3:160708200-160712000	Weak transcription	Placenta	Placenta
5	chr3:160710200-160712400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
6	chr3:160710600-160711600	Enhancers	Left Ventricle	heart
7	chr3:160711000-160711200	Enhancers	Stomach Smooth Muscle	stomach

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